Ships have a difficult time sampling the time and space scales relevant for understanding how the physics and chemistry regulates marine ecosystems (National Research Council 2000, 2003, Figure 3.1); therefore the biology in the oceans is chronically under-sampled. This is a major problem for policy makers and local governments charged with managing coastal resources who are increasingly being asked to develop ‘ecosystem-based management’ plans (US Ocean Commission on Ocean Policy, 2004). Th is is especially true in regions where Harmful Algal Blooms (HABs) are present (Hallegraeff, 1993). Ecosystem-based management requires a quantitative understanding of the processes controlling marine food webs. These processes include physical (mixing, stratifi cation, advection) and chemical (micro, macro, and organic nutrients) factors as well as trophic interactions within the marine food webs. These food-web interactions are especially difficult to study as they are modulated by complex climate (global warming, storms, winter cooling/summer heating), pelagic (mixing and stratifi cation), lithospheric (nutrient weathering), and anthropogenic (terrestrially derived macro and micro nutrients, buoyant plumes, human grazing pressures) forcing functions. Understanding these food webs requires an integrated view of physics, chemistry, and phytoplankton interactions.